This is follow-up information/questions to the issue I ran into with the galaxy
June 2nd, 2014 update. I hope to receive feedback on how to proceed.
- Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end
- When updating galaxy to the june 2nd release, the v120 DB schema has
referential integrity constraints, which produced errors during the upgrade.
- Completed two galaxy updates in the past 4 months without
encountering this before (schema changes included)
In the past, referential integrity in the DB schema was never an issue. I
checked backups and the current database to find that the database tables are
using the MyISAM engine. MyISAM = no referential integrity support, no
I reviewed galaxy's SQLAlchemy templates and determined that
mysql_engine='InnoDB' isn't set on tables. This explains why all tables were
created with the MyISAM engine. If the mysql_engine is not innodb, SQL Alchemy
is supposed to drop any referential integrity constraints defined in the
schema. What I don't understand is why SQL Alchemy is no longer ignoring the
referential integrity constraints.
Going forward, can anyone propose how I can salvage the database or continue
ignoring referential integrity for now?
Assuming that my limited understanding of SQLAlchemy holds water, I was looking
at fixing the galaxy code base but I need some clarification on the DB schema
versioning. Do I edit schema v1 and add the appropriate table args to make
every table an innodb engine table or do I add a new schema and modify all
tables to use the innodb engine? Alternatively, I can use DDL events
def after_create(target, connection, **kw):
connection.execute("ALTER TABLE %s ENGINE=InnoDB;
Thank you for your help.
Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
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